Soybeans Contain Plenty of B Vitamins, but Processing Removes Most of Them

Soybeans are naturally rich in vitamin B1 and vitamin B6, but much of that value is lost when they are processed into the protein powders used in many plant-based meat products, according to a new analytical study published in Food Production, Processing and Nutrition. Using a custom mass spectrometry technique, researchers measured individual vitamin forms in soybeans, soy protein concentrates and isolates, soymilk, and soy-based infant formula, and found that processing can remove 84 to 94 percent of the vitamins.

That matters because humans cannot make vitamins B1 and B6 on their own and must obtain them through food. As more people turn to plant-based diets, the nutritional makeup of these ingredients becomes increasingly important.

Accurately measuring these vitamins is more complicated than it first appears. Vitamin B6 is not a single substance but a group of related compounds, or vitamers, that differ greatly in how usable they are in the body. Pyridoxine (PN), pyridoxamine (PM), and pyridoxal (PL) are readily absorbed, while pyridoxine-5′-beta-D-glucoside (PNG), a plant-associated glycosylated form, has about half the bioavailability of PN. Standard tests usually measure only total vitamin B6 after hydrolysis, which can overstate what the body can actually use or miss glycosylated forms altogether. The new method combined strong cation exchange extraction with SelexION differential ion mobility separation on a triple quadrupole mass spectrometer, allowing the team to measure thiamine (vitamin B1) and individual B6 vitamers, including PNG and pyridoxamine-5′-phosphate (PMP), directly and without harsh hydrolysis steps.

The researchers validated the method carefully, using stable isotope-labeled internal standards to account for extraction losses and matrix effects, and confirmed linear calibration curves across the tested range. Recovery was acceptable for most targets, although pyridoxal, pyridoxal-5′-phosphate, and several other vitamers performed poorly and were left out. The team said the main benefit of the ion mobility approach was not higher sensitivity than an earlier beer-focused method, but better selectivity, which helps reduce background interference and false positives in complex foods.

When the method was applied to commercial soybeans, the vitamin profile was dominated by the less bioavailable PNG. Soybeans contained 3.9 to 7.1 micrograms of PNG per gram and 1.0 to 4.9 micrograms of thiamine per gram, while PN levels were about ten times lower and PM and PMP levels about twenty times lower. PNG made up roughly 84 percent of the total measured vitamin B6. Because PNG is estimated to be only about half as bioavailable as PN, the authors calculated that the effective bioavailability of vitamin B6 in soybeans is about 58 percent, in line with older absorption studies. By their estimate, about 339 grams of dry soybeans would be needed for women to meet the recommended daily intake of vitamin B6, and about 386 grams for men, with similar amounts needed for thiamine.

The difference in processed soy products was striking. Soy protein concentrates and isolates contained 84 to 94 percent less vitamin B1 and B6 than raw soybeans. PNG suffered the biggest loss, with protein extracts retaining only about 5 percent of soybean levels, followed by thiamine at 12 percent, PM at 15 percent, and PN at 16 percent. The balance of vitamers also shifted: PNG dropped from 84 percent of total B6 in soybeans to around 48 percent in concentrates and 50 percent in isolates. Based on the calculations, 3.5 kilograms of soy protein concentrate or 2.2 kilograms of soy protein isolate would be needed to reach the recommended vitamin B6 intake for women, and 7.3 kilograms or 2.5 kilograms, respectively, for enough thiamine.

There was also wide variation between individual protein products, with some powders containing fifty times less vitamin than soybeans and others only five times less, even though the study did not include full manufacturing details. When vitamin levels were compared with processing indicators, pH and the protein solubility index were positively associated with PNG, PN, and thiamine. Because a higher pH can point to alkaline treatment during extraction, the authors suggest that more intense alkaline processing may alter protein structures and increase binding to less polar vitamins, which could help retain them. Isolates, which typically undergo more alkaline treatment, contained significantly more vitamins than concentrates. The findings suggest that gentler processing methods that reduce exposure to heat, light, and other damaging conditions may preserve more vitamins, although the researchers caution that firm conclusions require direct knowledge of how each product was made.

Soymilk showed a different pattern. Non-fortified soymilk contained vitamin levels similar to soybeans, indicating that traditional soymilk production largely preserves naturally occurring vitamins, and it greatly outperformed almond and oat milk, which had almost no vitamin B1 or B6. Among the non-fortified samples, the freshest product, made three hours before purchase, had the highest levels, while an ultra-heat-treated soymilk had the lowest and showed no detectable PNG or PMP, suggesting that heat damages these nutrients. Two soymilk samples and the infant formulas were clearly fortified with pyridoxine and thiamine, showing elevated levels of only those vitamers. The measured amounts generally matched or slightly exceeded manufacturer declarations, which is a common way to ensure minimum nutrient levels through the end of shelf life.

The infant formula comparison was especially relevant for the Singapore-based researchers, where soy formula use is high. Both soy and cow milk formulas contained high levels of PN and thiamine from fortification, and far more thiamine than the poorly fortified soy formula linked to infant deaths in 2003, but they lacked the PM, PMP, and PNG found in soybeans, as well as the PM and PMP present in breast milk. The authors say fortification with PN and thiamine remains essential in all infant formulas, and that the effects of different vitamer profiles on infant development should be studied further. They also addressed concerns about too much B6, which can lead to neuropathy at high doses, calculating that more than three litres of the most fortified soymilk would be needed to reach even 6 milligrams per day, making excessive intake from soymilk unlikely.

The wider takeaway is that plant-based foods are not all nutritionally equivalent to the whole ingredients they come from. Soybeans and traditional soy foods do provide substantial amounts of B1 and B6, but industrial processing into protein isolates and concentrates removes most of these vitamins, and fortification replaces only PN and thiamine rather than the full range of vitamers whose functions are still not fully understood. Since PNG is less bioavailable than PN, diets heavy in soy may provide less usable vitamin B6 than total intake figures imply. The authors argue that plant-based products should be evaluated by their full vitamer profiles rather than by total vitamin content alone, and they call for more research on how PNG and other vitamers affect vitamin status in populations with low meat and low dairy intake.

Subject of Research: Quantification of vitamin B1 and B6 vitamer profiles in soybeans, soy protein products and soymilk using differential ion mobility mass spectrometry

Article Title: Quantification of B6 and B1 vitamers in soybeans, soy-protein and soymilk using a targeted differential ion-mobility mass spectrometry LCMS methodology

Article References: Watkins, O. C., Häuslein, C., Shu, W., Morsten, S., Poirier, C., Alpers, T., Becker, T., Park, J., Calvo-Baltanás, V., & Rychlik, M. (2026). Quantification of B6 and B1 vitamers in soybeans, soy-protein and soymilk using a targeted differential ion-mobility mass spectrometry LCMS methodology. Food Production, Processing and Nutrition, 8(1), Article 68. https://doi.org/10.1186/s43014-026-00416-6

Image Credits: AI Generated

Keywords: vitamin B1, vitamin B6, soybeans, soy protein isolate, soymilk, pyridoxine glucoside, thiamine, bioavailability, food processing, mass spectrometry, plant-based diet, fortification